MolNFT v1 · #156073 · protein
Crystal structure of bovine herpesvirus 1 glycoprotein D
6LS9 · Envelope glycoprotein D: “Crystal structure of bovine herpesvirus 1 glycoprotein D”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.82). MolNFT v1 #156073 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6LS9
- Type
- protein
- Length
- 721 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein D
- UniProt
- Q76PF1
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein D | protein | 241 | 18% helix, 31% strand | Q76PF1 |
| B | Envelope glycoprotein D | protein | 240 | 18% helix, 31% strand | Q76PF1 |
| C | Envelope glycoprotein D | protein | 240 | 18% helix, 31% strand | Q76PF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.82 | 0.83 | 111 | empty |
| 2 | 59 | 0.53 | 0.88 | 23 | empty |
| 3 | 159 | 0.50 | 0.78 | 20 | empty |
| 4 | 201 | 0.46 | 0.74 | 36 | empty |
| 5 | 136 | 0.41 | 0.75 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–C · 908 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 438 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6LS9 · Crystal structure of bovine herpesvirus 1 glycoprotein D · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q76PF1
- Elsewhere: RCSB PDB 6LS9 · PDBe 6LS9 · UniProt Q76PF1
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